Project name: 4AJY_L158P [mutate: LP158V]

Status: done

Started: 2020-09-18 14:35:10
Settings
Chain sequence(s) V: RPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIA
input PDB
Selected Chain(s) V
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues LP158V
Energy difference between WT (input) and mutated protein (by FoldX) -1.13615 kcal/mol
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with V chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       FoldX:    Building mutant model                                                       (00:01:40)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:46)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:35)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:26:08)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:26:08)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:26:09)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:26:10)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:26:10)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:26:11)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:26:12)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:26:13)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:26:13)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:26:14)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:26:15)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:26:16)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:26:16)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:26:17)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:26:18)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:26:18)
[INFO]       Main:     Simulation completed successfully.                                          (00:26:19)
Show buried residues
Minimal score value
-4.1808
Maximal score value
1.7014
Average score
-0.8212
Total score value
-121.5334
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
60 R V -1.7899
61 P V -0.8569
62 V V 0.8552
63 L V 0.0000
64 R V -1.0764
65 S V 0.0000
66 V V -0.2682
67 N V -1.0505
68 S V -1.3862
69 R V -2.3840
70 E V -1.7018
71 P V -1.1561
72 S V 0.0000
73 Q V -0.9603
74 V V 0.0000
75 I V -0.6808
76 F V 0.0000
77 C V 0.0000
78 N V 0.0000
79 R V -2.2267
80 S V 0.0000
81 P V -0.6082
82 R V -0.1399
83 V V 0.7862
84 V V 0.0000
85 L V 0.2361
86 P V 0.0000
87 V V 0.0000
88 W V -0.2707
89 L V 0.0000
90 N V -1.2688
91 F V -1.1427
92 D V -2.4886
93 G V -1.9525
94 E V -2.7812
95 P V -1.6176
96 Q V -0.9573
97 P V -0.2171
98 Y V 0.2875
99 P V -0.0119
100 T V 0.1699
101 L V 0.0000
102 P V -0.3017
103 P V -0.7634
104 G V -1.2364
105 T V -0.9910
106 G V -1.4659
107 R V -1.5540
108 R V -2.1453
109 I V -1.2456
110 H V -1.2866
111 S V 0.0000
112 Y V -0.6733
113 R V -0.6301
114 G V -0.0425
115 H V 0.0000
116 L V 0.6711
117 W V 0.0000
118 L V 0.0000
119 F V 0.0000
120 R V 0.0000
121 D V 0.0000
122 A V -0.0518
123 G V -0.3779
124 T V -0.7001
125 H V -0.8268
126 D V 0.0000
127 G V -0.2440
128 L V 0.0000
129 L V -0.0762
130 V V 0.0000
131 N V -1.0627
132 Q V -1.4149
133 T V -0.8627
134 E V -0.5979
135 L V 0.1849
136 F V 0.0000
137 V V 1.2599
138 P V 0.0000
139 S V 0.5594
140 L V 0.6273
141 N V 0.0244
142 V V 0.5601
143 D V -1.4647
144 G V -1.3281
145 Q V -1.2387
146 P V -0.5699
147 I V 0.6918
148 F V 0.4851
149 A V 0.0000
150 N V -0.9053
151 I V 0.0000
152 T V -0.5853
153 L V 0.5079
154 P V 0.9416
155 V V 1.7014
156 Y V 0.2924
157 T V -0.6088
158 P V -1.0704 mutated: LP158V
159 K V -1.8363
160 E V -1.8418
161 R V -1.3468
162 C V -0.3263
163 L V 0.0000
164 Q V 0.0000
165 V V 0.9381
166 V V 0.8914
167 R V -0.1694
168 S V 0.5449
169 L V 1.3861
170 V V -0.4311
171 K V -2.1651
172 P V -2.5907
173 E V -3.4167
174 N V -3.1105
175 Y V 0.0000
176 R V -3.5327
177 R V -3.2525
178 L V -1.7122
179 D V -1.8946
180 I V -0.1124
181 V V 0.7769
182 R V -1.5909
183 S V -0.9012
184 L V -1.0374
185 Y V 0.0000
186 E V -3.4497
187 D V -2.8746
188 L V 0.0000
189 E V -3.3808
190 D V -3.4846
191 H V -2.9026
192 P V -1.9334
193 N V -2.1483
194 V V -1.8169
195 Q V -3.0216
196 K V -3.2969
197 D V -2.7504
198 L V 0.0000
199 E V -4.1016
200 R V -4.1808
201 L V -2.5110
202 T V -1.9447
203 Q V -2.5858
204 E V -2.9483
205 R V -1.5502
206 I V 0.7955
207 A V -0.2414
Download PDB file
View in 3Dmol
Play the video

CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.8212 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A3D Score
input -0.8212 View CSV PDB
model_3 -0.8773 View CSV PDB
model_0 -0.8853 View CSV PDB
model_4 -0.9116 View CSV PDB
model_8 -0.9197 View CSV PDB
model_7 -0.9264 View CSV PDB
model_2 -0.9533 View CSV PDB
model_1 -0.9693 View CSV PDB
model_11 -0.9767 View CSV PDB
model_9 -0.9947 View CSV PDB
model_6 -1.0302 View CSV PDB
model_10 -1.0468 View CSV PDB
model_5 -1.1011 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018